HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties.
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TLDR
This method uses a convex hull model to estimate the hydrodynamic volume of the molecule and is orders of magnitude faster than common methods and works well for both folded proteins and ensembles of conformationally heterogeneous proteins and for nucleic acids.About:
This article is published in Biophysical Journal.The article was published on 2018-02-27 and is currently open access. It has received 112 citations till now.read more
Citations
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RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation
Jordina Guillén-Boixet,Andrii Kopach,Alex S. Holehouse,Sina Wittmann,Marcus Jahnel,Marcus Jahnel,Raimund Schlüßler,Kyoohyun Kim,Irmela R.E.A. Trussina,Jie Wang,Daniel Mateju,Ina Poser,Shovamayee Maharana,Martine Ruer-Gruß,Doris Richter,Xiaojie Zhang,Young-Tae Chang,Jochen Guck,Alf Honigmann,Julia Mahamid,Anthony A. Hyman,Rohit V. Pappu,Simon Alberti,Simon Alberti,Titus M. Franzmann +24 more
TL;DR: It is proposed that condensation coupled to conformational rearrangements and heterotypic multivalent interactions may be a general principle underlying RNP granule assembly.
Journal ArticleDOI
Unraveling Molecular Interactions in Liquid-Liquid Phase Separation of Disordered Proteins by Atomistic Simulations.
TL;DR: This work exploited explicit-solvent atomistic simulations to investigate the N-terminal disordered region of DEAD-box helicase 4 (NDDX4) and determined NDDX4 conformational ensemble at the single-molecule level, providing a high-resolution picture of the molecular mechanisms underlying phase separation in agreement with NMR and mutagenesis data.
Journal ArticleDOI
Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics.
Jeong-Mo Choi,Rohit V. Pappu +1 more
TL;DR: An improved version of the ABSinTH implicit solvation model and force field paradigm is presented by incorporating a grid-based term that bootstraps against experimentally derived and computationally optimized conformational statistics for blocked amino acids to demonstrate the robustness of ABSINTH-C.
Journal ArticleDOI
Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods.
Mustapha Carab Ahmed,Line K Skaanning,Alexander Jussupow,Estella A. Newcombe,Birthe B. Kragelund,Carlo Camilloni,Carlo Camilloni,Annette Eva Langkilde,Kresten Lindorff-Larsen +8 more
TL;DR: In this paper, the authors apply metainference and Bayesian/maximum entropy reweighting approaches to integrate prior knowledge of the system with experimental data, while also dealing with various sources of errors and the inherent conformational heterogeneity of intrinsically disordered proteins.
Posted ContentDOI
Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions
TL;DR: A novel multiscale chromatin model is developed that integrates atomistic representations, a chemically-specific coarse-grained model, and a minimal model to achieve enhanced sampling of high-resolution chromatin and finds that nucleosome thermal fluctuations become significant at physiological salt concentrations and destabilize the 30-nm fiber.
References
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The quickhull algorithm for convex hulls
TL;DR: This article presents a practical convex hull algorithm that combines the two-dimensional Quickhull algorithm with the general-dimension Beneath-Beyond Algorithm, and provides empirical evidence that the algorithm runs faster when the input contains nonextreme points and that it used less memory.
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Voronoi diagrams—a survey of a fundamental geometric data structure
TL;DR: The Voronoi diagram as discussed by the authors divides the plane according to the nearest-neighbor points in the plane, and then divides the vertices of the plane into vertices, where vertices correspond to vertices in a plane.
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Classification of intrinsically disordered regions and proteins.
Robin van der Lee,Robin van der Lee,Marija Buljan,Benjamin Lang,Robert J. Weatheritt,Gary W. Daughdrill,A. Keith Dunker,Monika Fuxreiter,Julian Gough,Joerg Gsponer,David T. Jones,Philip M. Kim,Richard W. Kriwacki,Christopher J. Oldfield,Rohit V. Pappu,Peter Tompa,Peter Tompa,Vladimir N. Uversky,Vladimir N. Uversky,Peter E. Wright,M. Madan Babu +20 more
TL;DR: Characterization of unannotated and uncharacterized protein segments is expected to lead to the discovery of novel functions as well as provide important insights into existing biological processes and is likely to shed new light on molecular mechanisms of diseases that are not yet fully understood.